Background: Malaria is a significant health burden for many countries worldwide. Insecticide-treated bed nets and mosquito repellent are considered effective methods for preventing Anopheles bites. However, changes in the biological properties of the vector have led to a reduction in their effectiveness. The vector has been studied, but the behaviour has been poorly examined. Therefore, this study aims to investigate the importance of primary vector activity for selecting an appropriate malaria protection strategy. Methods: Initially, active case detection (ACD) was carried out in western and eastern parts of Indonesia, Jambi and Sumba, to confirm their endemicity level. According to the 2016 national health report of Indonesia, Jambi has an annual parasite index (API) of 0.14 and Sumba has an API of 5.41. A series of entomological observations were carried out to compare the biting activity of Anopheles vectors in two localities, with a total of 216 houses and 216 catchers (108 at each study site). Results: The results indicated that endemicity at the sub-district level is higher than that at the provincial level. Only Anopheles balabacensi was found to be exophagic. Multiple comparisons found different biting times between the sites, suggesting that early evening (18.00-20.00) is most likely to be the time when mosquitoes transmit the Plasmodium parasite in Jambi, while during sleeping hours (21.00-01.00) is the peak biting time of Anopheles mosquitoes in Sumba. Conclusions: The study demonstrates the importance of Anopheles species blood feeding patterns in selecting an appropriate malaria protection strategy.